I recently had some kind of "similar" (but in my case much more fortunate) situation. BKK-DXB-ZRH (return flight), the segment BKK-DXB got cancelled after they plane had an issue (we were in the plane, waiting for 2 hours till they cancelled it eventually, the treatment on the ground was very bad but never mind, that's not the issue here)

I got rebooked on the next flight, and due to 8 hours transit in DXB I still made the connection as the next flight left only 6 hours after the original schedule. I never had such a tight connection with a long connection baggage tag for sure

Anyway, the miles for the flights never posted, even though the system knew I had them booked/flown/whatever (I could claim missing miles, they showed up but never got credited)

Called EK 2 weeks after the flights, the callcenter guy told me that I've never flown the DXB-ZRH leg. Emmmm, what? Seems that because somehow their system got crazy after cancelling the original BKK-DXB flight they never automatically realised to "protect" the second leg. I could board the flight regularely anyway, so the system itself didn't cancelled it, they just said I've never flown the segment (For whatever reasons, they thought I was still hanging around in DXB for 2 weeks.. probably they would have called immigration soon )

So, from my experience, it seems EK does have some issues with their system regarding re-booking of pax due to "different" situations. Which is what most say about EK, great in the air, crap on the ground in case anything goes wrong.